Biological enzyme catalysts, such as P450BM-3 enzymes, find increasing use in a variety of industrial applications, ranging from synthesis of fine chemicals, intermediates, pharmaceuticals and drug metabolites to degradation of organic chemical contaminants and pollutants. Protein engineering, using directed evolution or site-directed mutagenesis, can be used to isolate variants of known enzymes, which may create new opportunities and applications for their catalytic activities.
P450BM-3 from Bacillus megaterium (1) belongs to the superfamily of cytochrome P450 enzymes. There are over 7,700 genes encoding P450 enzymes in the various gene sequence databases. Nomenclature of P450 enzymes has been systemized. The superfamily of enzymes are referred to as CYP, followed by a number for a family of enzymes (hence CYP1, CYP51, CYP102, etc.) which are divided into subfamilies denoted by alphabets (hence CYP1A, CYP101B, etc.) and each sub-family member is denoted by a number (hence CYP1A1, CYP3A4, CYP101D3, etc.). A gene encoding a CYP enzyme is denoted by italics, e.g. CYP101A1 gene. P450BM-3 has been designated CYP102A1, i.e. it is the first member of the CYP102 family. Henceforth the systemic name of CYP102A1 will be used for P450BM-3.
CYP102A1 (1) is an attractive enzyme for biotransformation applications because it is catalytically self-sufficient. Unlike other P450 enzymes, in which the P450 monooxygenase and the electron transfer co-factor proteins are separate entities, CYP102A1 has the haem monooxygenase domain fused to the diflavin electron transfer reductase domain, which contains both the FAD and FMN prosthetic groups in a single polypeptide. The natural substrates of CYP102A1 are believed to be linear or branched medium chain fatty acids (1,2). The crystal structure of the CYP102A1 haem domain became available in 1993 (3), revealing the active site structure and the presence of a substrate access channel. The crystal structure with a bound substrate, published four years later, indicated a change in the side chain conformation for F87 upon substrate binding (4).
Protein engineering of CYP102A1 has been reviewed (5-7). Early studies focused on the active site residue F87, with the F87V, F87A, F87Y and F87G mutations showing varied effects on the activity and selectivity of fatty acid oxidation (8-11). Mutations at F87 have been found to be beneficial to the oxidation of a variety of substrates (7). Residues such as F42, R47, and Y51 at the entrance to the substrate access channel were also targeted. Neutralizing or reversing the charge at the 47 position altered the substrate specificity (8,12), as did the hydrophobic substitution Y51A, while the F42A mutation lowered enzymatic activity (10). WO0031273 disclosed the use of the R47L/Y51F couplet of mutations to promote entry, binding and oxidation of hydrophobic organic molecules such as polyaromatic and terpenoid hydrocarbons. The couplet was also combined with the F87A, I263A, A264G and M354A mutations to give enhanced activity and/or product selectivity of substrate oxidation (13,14). The R47L/Y51F combination, and the R47L and Y51F mutations on their own, are now commonly used in CYP102A1 engineering (15-19).
In addition to rational selection of mutation sites, screening techniques have been utilized to identify other mutations and mutation sites which have desirable effects on activity and selectivity. Random or site saturation mutagenesis was applied to CYP102A1 as early as 1997 (20). NO20020380 disclosed the use of indigo formation via indole oxidation as a screening method to discover CYP102A1 mutants with new activity. Saturation mutagenesis was applied to a number of residues likely to affect substrate binding, and the mutant A74G/F87V/L188Q was reported to oxidize a wide range of organic molecules with enhanced activity and altered selectivity compared to the wild type (21-25). AT342351T disclosed the formation of p-nitrophenol, which is spectroscopically detected, via oxidation of a ω-p-nitrophenoxy-carboxylic acid, as a screening procedure in a set of random mutagenesis experiments. The mutations V26T, R47F, S72G, A74G, F87A&V, L188A,G,N,K,Q,R,S&W, M354T were disclosed (26,27).
The p-nitrophenol screening method was extended by using p-nitrophenoxyoctane as the surrogate substrate. WO2002083868, EP1470219 and US2005202419 (subsequently corrected in WO2005017116, EP1660646, and US2005037411) disclosed the mutations L52I, I58V, F87A, H100R, S106R, F107L, A135S, M145A&V, A184V, N239H, S274T, L324I, V340M, I366V, K434E, E442K, V446I.
WO2003008563 and US2003100744 disclosed the results of further rounds of random mutagenesis, gene shuffling and screening using the same method, and reported the mutations M30I, E64A, V78A, F87A,D,G,H,I,K,N,R,V&W, H138Y, F162S, H171Q, T175I, V178I, A184V, N186D, D217V, I220T, K224I, S226I, D232G, T235A, H236Q, E252G, R255S, I258T, I259V, T268Q, A290V, A295T, L353V, D370Q, E380G, G396M, T411A, M416L.
WO2005017105, US2005059128, and EP1639091 disclosed the use of the same methods and reported the mutations R47C, L75I&W, V78A,F&T, A82L,F,G,I,S&T, F87I,L&V, T88C, K94I, P142S, T175I, A184V, F205C, S226R, H236Q, E252G, R255S, T260,L,N&S, A290V, A328V&M, L353V.
WO2006105082 then disclosed the mutations R47C, V78F, A82S, K94I, P141S, T175I, A184V, F205C, S226R, H236Q, E252G, R255S, A290V, A291V, A328F, L353V.
These series of mutants generated by random mutagenesis show enhanced activity for the oxidation of alkanes from ethane to medium chain alkanes (28-30). There were also selectivity changes, in particular when the directed evolution variants were combined with mutations introduced into the active site by site-directed mutagenesis, e.g. in octane oxidation where the mutations shift the site of oxidation towards the terminal carbon (31), selective epoxidation of terminal alkenes (32), and enantioselectivity in the oxidation of cyclopentanecarboxylic acid derivatives (33). It is notable that better results can often be obtained by combining directed evolution with rational re-design.
CYP102A3 is a P450 enzyme in the same sub-family as CYP102A1. Random mutagenesis of CYP102A3, followed by alkane oxidation and monitoring NADH formation in the presence of an alcohol dehydrogenase specific for terminal alcohols, gave rise to a mutant that formed 50% 1-octanol from octane oxidation. This is the highest proportion of terminal C—H bond oxidation of a linear alkane observed to date by an engineered CYP102 family P450 enzyme (34).
There is a continuing need to isolate further mutants of industrially useful enzymes, such as CYP102A1 enzymes, in order to further understand the impact of structural changes on their catalytic mechanism, improve their catalytic turnover, and expand their range of substrates and/or products. In general, engineering of P450 enzymes such as CYP102A1 is carried out to enhance enzymatic activity, with control of product selectivity and substrate specificity being important secondary objectives. Mutations and mutation sites which can couple selectivity control to enhanced monooxygenase activity are conspicuously lacking, such that enzymatic turnover of compounds may be fast but not sufficiently selective, or there is some selectivity but the reactions are slow, or the desired product is not formed. There is also a need for screening methods that can provide mutants with enhanced activity and/or desirable selectivity.